Lecture 4 Flashcards
(20 cards)
Difference between stick view and cartoon view
shows each atom vs highlights secondary structure
Describe the reaction when acetic acid is in water
we end up with an equilibrium, some dissociates into conjugate base (with H removed) and some stays as acetic acid - acetic acid easily loses a proton (acetate is resonance stabilized)
At what pH and pKa do we have equal amount of species?
pH = 1, pKa = 4.75
What are the net charges on acidic residues and basic residues?
Net negative charge at pH 7, net position charge at pH 7
describe acidic residues
Uncharged in their protonated states and negatively charged in their deprotonated states
describe basic residues
Positively charged in their protonated states and uncharged in their deprotonated states
What are the three types of basic amino acids?
Lysine, arginine, histidine
Equilibrium direction of lysine
Lies to the left, positively charged at 7
Why is lysine basic?
Amines are very basic
Why is arginine basic?
has a guanidinium group that is resonance stabilized in its protonated state
Equilibrium direction of arginine
Lies far to the left
Why is histidine unusual among the basic residues? What does this mean?
pKa is close to 7. Both protonated and deprotonated states are common
What is the isoelectric point?
point at which we have a net zero charge on our protein. All the negatives and positives all add up to zero - net charge of 0
What does the energy of the interaction between two charges depend on? (3)
- The magnitude of the charges (the value and sign of q)
- The distance between them ( r )
- The nature of the media between them (D = dielectric constant)
What is the job of cytochrome b5? How does this happen?
protein that transfers electrons to cytochrome c. The two proteins have to dock together
Polarity and charge of aromatic residues:
nonpolar and uncharged
List the aromatic residues:
Phenylalanine, tyrosine, tryptophan
Where do aromatic amino acids absorb light and what is maximum absorbance?
absorb light in the UV region of the spectrum with maximal absorbance near 280nm
what does the absorption of UV radiation at 280nm causes electrons in aromatic ring to do?
jump from lower-energy pi-orbitals to higher-energy pi-antibonding orbitals
In a protein chain, what is the first residue?
Methionine
